My research program examines neurophysiological substrates of cognition and emotion in depression and anxiety through the lifespan using self-report, behavioral, physiological, and neuroimaging (fMRI) assessment, as well as computational modeling. A specific goal of this work is to better understand what cognitive and brain processes predict and change with recovery, and how to improve treatments by targeting these mechanisms more directly. The role of sustained emotional information processing (e.g., rumination) is a particular focus of this work. For more detailed information, check out a more
detailed description of my research and my
vita.

Guidelines papers for psychophysiology for reporting on psychophysiological studies of all types including heart rate variability, startle, EMG, heart rate, EEG, MEG, ERPs, blood pressure, GSR, etc. They are at the bottom of the page - scroll all the way down.

Software for distribution

Pupillary waveform deblinking Matlab code identifies and linearly interpolates through blinks in a waveform of pupillary motility data. Usually works on eyetracking data as well as other relatively physiological waveforms scaled appropriately.

Waveform comparisons Matlab code implements tests to compare physiological waveforms at every sample, as used in a bunch of my lab's publications. Please install all directories in your matlab path and do check out the documention in the pupil_toolkit_waveform_comparisons.pdf file in the main directory.

Software for use in collaboration, not available for download. Not distributed without individual consultation and discussion

My lab uses a great deal of "home grown" software. Many people ask whether they can use it to. The answer is generally yes, but it will take some work. The software is fit for use by engineers or highly trained people, and is not prime-time. It works. It is often not well documented. There are no graphic interfaces. It all takes programming in matlab or Unix scripting. As such, if you are going to request to use it please 1) have a matlab-savvy engineer type on hand (I cannot do tech support) and 2) expect to work closely with me in implementing your stream, at least at first. If you are interested in this type of arrangement, please feel free to talk to me about possible collaboration on your projects. Unfortunately my time is somewhat limited so I cannot afford to distribute this collection of hacks widely. Some of the software libraries we use, and what it would likely take for your group to also use them are described below as examples. Note that I have overengineered the process for getting involved with this code only so that when we are done, we can all be sure that what is coming out of the code is right for your lab.

The Pupil Toolkit. This is the motly collection of matlab code my lab uses to analyze our pupil data. Typically, using it involves either you visiting my lab or me visiting you for a day or two, working to make sure we can read your data, and process it, and writing example scripts together. This process has worked for many labs.

Emotiv Headset processing code. This is a collection of Matlab routines built on the FieldTrip and EEGlab matlab platforms. It implements a number of steps for processing data from the Emotiv Headset in a way that ERP and EEG data are interpretable and often comparable to data from much more expensive systems. Publications are forthcoming. It is a work in progress. Typically using it involves entering into a formal collaborative relationship where we are all authors on papers using the code. Site visits are a must.

fMRI code. This is a collection of scripts, c-source code, and matlab code used by our lab to process our fMRI data. Mostly we work on top of NIS and AFNI. If you want to use our code independently, as we do it, please consider doing a post-doc in my lab. That said, if you are using one of the fMRI tasks developed in my group and want to know whether your results would match ours if you just processed the data like we do, we are frequently up for re-analyzing your data, in collaboration with you.

For inquiring minds: For the Siegle et al (2006) American Journal of Psychiatry treatment prediction paper, the BA25 ROI was centered around Talariach coordinates: 6, 17, -6 and extended from 6,17,-2 to 7,19,-11. The Amygdala ROI was maximal at 15,-3,-15 and extended from 13,-3,-14 to 19,-4,-17.

Here's an animation showing the mean of 25 control participants' brain activity associated with rating the personal relevance of positive words. The animation was made by generating a snapshot of regions significantly different (p<0.001) from the pre-trial baseline at each TR (1.5 seconds) for the 12 second trial (in AFNI), and interpolating between them (in Virtual Dub). As shown in the animation the anterior cingulate reacts early, followed slightly later by BA47, a brain region associated with rumination. Data from Siegle, G.J., Thompson, W., Thase, M.E., Steinhauer, S.R., Carter, C. S., (in press). Increased amygdala and decreased dorso-lateral prefrontal BOLD responses in unipolar depression: Related and independent features. Biological Psychiatry. Animation by Greg Siegle and Lena Gemmer.

Here's an animation showing the location of the amygdala. Roma Konecky and I made this from an SPGR image acquired on a 1.5T GE scanner
using BrainVoyager to align and smooth the image, MRICro to trace the amygdala, AFNI to create the rendering, and WWW Gif Animator to concatenate the frames.